Object createAtomSetCollectionFromString(
String strModel, Map<String, Object> htParams, boolean isAppend) {
setLoadState(htParams);
boolean isAddH = (strModel.indexOf(JC.ADD_HYDROGEN_TITLE) >= 0);
String[] fnames = (isAddH ? getFileInfo() : null);
FileReader fileReader =
new FileReader(
this,
viewer,
"string",
"string",
"string",
null,
JmolBinary.getBR(strModel),
htParams,
isAppend);
fileReader.run();
if (fnames != null) setFileInfo(fnames);
if (!isAppend && !(fileReader.getAtomSetCollection() instanceof String)) {
viewer.zap(false, true, false);
setFileInfo(
new String[] {strModel == JC.MODELKIT_ZAP_STRING ? JC.MODELKIT_ZAP_TITLE : "string"});
}
return fileReader.getAtomSetCollection();
}
/**
* not used in Jmol project -- will close reader
*
* @param fullPathName
* @param name
* @param reader
* @param htParams
* @return fileData
*/
Object createAtomSetCollectionFromReader(
String fullPathName, String name, Object reader, Map<String, Object> htParams) {
FileReader fileReader =
new FileReader(this, viewer, name, fullPathName, name, null, reader, htParams, false);
fileReader.run();
return fileReader.getAtomSetCollection();
}
/*
* note -- createAtomSetCollectionFromXXX methods
* were "openXXX" before refactoring 11/29/2008 -- BH
*
* The problem was that while they did open the file, they
* (mostly) also closed them, and this was confusing.
*
* The term "clientFile" was replaced by "atomSetCollection"
* here because that's what it is --- an AtomSetCollection,
* not a file. The file is closed at this point. What is
* returned is the atomSetCollection object.
*
* One could say this is just semantics, but there were
* subtle bugs here, where readers were not always being
* closed explicitly. In the process of identifying Out of
* Memory Errors, I felt it was necessary to clarify all this.
*
* Apologies to those who feel the original clientFile notation
* was more generalizable or understandable.
*
*/
Object createAtomSetCollectionFromFile(
String name, Map<String, Object> htParams, boolean isAppend) {
if (htParams.get("atomDataOnly") == null) {
setLoadState(htParams);
}
name = viewer.resolveDatabaseFormat(name);
int pt = name.indexOf("::");
String nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
String fileType = (pt >= 0 ? name.substring(0, pt) : null);
Logger.info(
"\nFileManager.getAtomSetCollectionFromFile("
+ nameAsGiven
+ ")"
+ (name.equals(nameAsGiven) ? "" : " //" + name));
String[] names = classifyName(nameAsGiven, true);
if (names.length == 1) return names[0];
String fullPathName = names[0];
String fileName = names[1];
htParams.put(
"fullPathName",
(fileType == null ? "" : fileType + "::") + fullPathName.replace('\\', '/'));
if (viewer.getBoolean(T.messagestylechime) && viewer.getBoolean(T.debugscript))
viewer.scriptStatus("Requesting " + fullPathName);
FileReader fileReader =
new FileReader(
this, viewer, fileName, fullPathName, nameAsGiven, fileType, null, htParams, isAppend);
fileReader.run();
return fileReader.getAtomSetCollection();
}
